cyjShiny

cyjShiny provides network visualization within Shiny applications and R Markdown documents for exploration and presentation of graph-structured biological data.

Key Features:

• cytoscape.js integration: Leverages the cytoscape.js JavaScript graph library to render graph visualizations.
• R–JavaScript bridge (Shiny): Exposes an R-to-JavaScript interface enabling embedding of cytoscape.js components into Shiny applications and R Markdown outputs.
• Data conversion utilities: Includes helper functions to convert R data structures such as data.frame into formats compatible with cytoscape.js.

Scientific Applications:

• Bioinformatics and systems biology network visualization: Visualizing molecular interaction and other biological networks for analysis.
• Exploratory data analysis: Inspecting graph topology, node and edge attributes, and connectivity patterns to inform downstream analyses.
• Hypothesis generation and presentation: Generating hypotheses from network structure and embedding visualizations into reports and publications.

Methodology:

Builds upon the cytoscape.js library and provides an R–JavaScript bridge via Shiny, with helper functions converting R data.frame objects into cytoscape.js-compatible formats.